Executing Python commands in a blender subprocess
Invoke blender with the --help option to get all available options.

In your case you might simply use the --python option to load a script. 
Note: The order of the arguments are given in is important.


.\blender.exe Subprocess.blend --python your_script.py


or

subprocess.Popen([blenderPath, , "Subprocess.blend", "--python", "your_script.py"])


This way the blended is loaded first and then the python script is executed.


Blender 2.78 (sub 0)
Usage: blender [args ...] [file] [args ...]

-P or --python 
    Run the given Python script file

--python-text 
    Run the given Python script text block

--python-expr 
    Run the given expression as a Python script

Argument Parsing:
    Arguments must be separated by white space, eg:
    # blender -ba test.blend
    ...will ignore the 'a'
    # blender -b test.blend -f8
    ...will ignore '8' because there is no space between the '-f' and the frame value

Argument Order:
    Arguments are executed in the order they are given. eg:
    # blender --background test.blend --render-frame 1 --render-output '/tmp'
    ...will not render to '/tmp' because '--render-frame 1' renders before the output path is set
    # blender --background --render-output /tmp test.blend --render-frame 1
    ...will not render to '/tmp' because loading the blend-file overwrites the render output that was set
    # blender --background test.blend --render-output /tmp --render-frame 1
    ...works as expected.


By the way, I think you don't need the -r option.


-r 
    Silently register blend-file extension, then exit (Windows only)